vmd ships with a tool, catdcd, which is very useful for converting molecular dynamics trajectories from one format to another. It would be nice to have catdcd added to the PATH, but that's not critically important. The problem is that catdcd segfaults immediately upon trying to run it. I wonder if this is related in some way to the extra patches Gentoo bundles with vmd. Reproducible: Always Steps to Reproduce: Run catdcd (with no arguments) Actual Results: $ /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd Segmentation fault Expected Results: Print usage information I tried recompiling with debugging info... CFLAGS="-march=native -O2 -pipe -ggdb3" CXXFLAGS="${CFLAGS}" FEATURES="splitdebug compressdebug installsources" emerge -1 vmd ...and this is the result in gdb: $ gdb -q /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd Reading symbols from /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd... Reading symbols from /usr/lib/debug//usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd.debug... (gdb) r Starting program: /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd Program received signal SIGSEGV, Segmentation fault. 0x0000000000000001 in ?? ()
Is there not more in the backtrace?
Nope, that's all there is. Some googling suggested that this might happen when you try to execute a shared library, which makes me wonder if it's being linked incorrectly.
It is the same issue even without applying the plugins patch :/
This is still a problem in 1.9.4_alpha57
I was playing with the plugins directory, and with a small change to remove the hardcoded tcl version, the plugins directory compiles fine on my system and catdcd runs without issues. So, the segfault is related to either the ebuild or the context of compiling the plugins as part of the overall VMD compilation.